I've always thought of "The Way of the Warrior" as having the look and feel of a second pilot as well. It certainly did the job of breathing new life into the series - the Klingon arc was arguably one of the bravest decisions to make at that point.
There's a line in a season five two-parter where Gowron says something like the following:
"Think of it, Captain! Four years ago no one had ever heard of Bajor or Deep Space Nine, and now all our hopes rest here. Where the tides of fortune take us, no man can tell."
It's one of the defining lines of the series in my view, and really sums up one of the great things about the show, which is how it keeps expanding and building on its original premise. For example, season two is a great season, one of the best of the series, but when you compare it to the epic scale of the later seasons, it's almost hard to believe its part of the same show. Not that all the later seasons are necessarily better, but they do take place on a far grander scale.
DS9 just keeps ratcheting up the intensity and the complexity over and over throughout its run.
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